# List of top-scoring protein chains for t2k-100-30-near-backbone-11-scores hidden Markov model. # HMM and HMM E-value scores computed by SAM (c) 1992-2001 Regents of the University of California, Santa Cruz # Sequence Alignment and Modeling Software System # http://www.cse.ucsc.edu/research/compbio/sam.html # ----------------- Citations (SAM, SAM-T99, HMMs) -------------------- # R. Hughey, A. Krogh, Hidden Markov models for sequence analysis: # Extension and analysis of the basic method, CABIOS 12:95-107, 1996. # K. Karplus, C. Barrett, R. Hughey, Hidden Markov models for detecting # remote protein homologies, Bioinformatics 14(10):846-856, 1998. # A. Krogh et al., Hidden Markov models in computational biology: # Applications to protein modeling, JMB 235:1501-1531, Feb 1994. # # FSSP representative for each protein chain taken from FSSP: # ------------------Citations (FSSP) ----------------------------------- # L. Holm and C. Sander (1996) Mapping the protein universe. Science 273:595-602. # #SCOP domains found in each protein chain taken from SCOP: # ------------------Citations (SCOP) ----------------------------------- #Murzin A. G., Brenner S. E., Hubbard T., Chothia C. (1995). #SCOP: a structural classification of proteins database for the investigation of sequences and structures. #J. Mol. Biol. 247, 536-540. Sequence_ID Length Target_Evalue FSSP-rep SCOP_domain SCOP_suid 5S 5N 12S 6S 12S 10N 1mjhA 162 8.88e-02 1mjhA c.26.2.4 31639 1mjhB 162 9.51e-02 1mjhA c.26.2.4 31640 1eh9A 558 4.05e-01 1ehaA b.1.18.2,b.71.1.1,c.1.8.1 21858,27785,28772 2anuA 255 5.51e-01 1ehaA 558 6.20e-01 1ehaA b.1.18.2,b.71.1.1,c.1.8.1 21859,27786,28773 1ps9A 671 8.81e-01 c.1.4.1,c.3.1.1,c.4.1.1 95076,95077,95078 1vdkA 466 9.17e-01 a.127.1.1 100561 1a4iB 301 1.00e+00 1a4iA c.2.1.7,c.58.1.2 30279,33927 1diaA 306 1.38e+00 1a4iA c.2.1.7,c.58.1.2 30280,33928 1a4iA 301 1.51e+00 1a4iA c.2.1.7,c.58.1.2 30278,33926 1n81A 186 2.04e+00 a.185.1.1 85388 1nbaA 264 2.08e+00 1nbaA c.33.1.3 31753 1w0mA 226 2.12e+00 c.1.1.1 109027 1tqgA 105 2.12e+00 a.24.10.3 107224 1uqrA 154 2.28e+00 c.23.13.1 99779 1q7rA 219 3.03e+00 c.23.16.1 96054 3pga1 337 3.43e+00 4pgaA 1xfiA 367 3.61e+00 e.50.1.1 109584 1yb0A 159 4.06e+00 1vl8A 267 4.26e+00 c.2.1.2 108733 1brlA 355 4.31e+00 1lucA c.1.16.1 29553 1xzoA 174 5.32e+00 1z41A 338 5.54e+00 1l4uA 176 5.97e+00 c.37.1.2 73568 1agp 166 6.03e+00 1ctqA c.37.1.8 31985 1r85A 379 6.14e+00 c.1.8.3 104839 1ctqA 166 6.23e+00 1ctqA c.37.1.8 31965 1mv8A 436 6.29e+00 a.100.1.4,c.2.1.6,c.26.3.1 85128,85129,85130 1khyA 148 6.31e+00 a.174.1.1 77410 821p 166 6.64e+00 1ctqA c.37.1.8 31969 1lxkA 721 7.00e+00 a.102.3.2,b.24.1.1,b.30.5.2 74331,74332,74333 2minA 491 7.00e+00 1qguA c.92.2.3 35609 1lehA 364 7.20e+00 1bw9A c.2.1.7,c.58.1.1 30268,33916 1eguA 731 7.33e+00 1eguA a.102.3.2,b.24.1.1,b.30.5.2 18850,23899,24423 1o9iA 266 7.59e+00 a.25.1.3 92671 1ubeA 349 7.63e+00 c.37.1.11,d.48.1.1 88412,88413 3minC 491 7.67e+00 1qguA c.92.2.3 35607 1lh0A 213 8.28e+00 c.61.1.1 73896 1jkvA 266 8.49e+00 a.25.1.3 71719 1vdxA 184 8.81e+00 1php 394 9.19e+00 16pk c.86.1.1 35452 1vjgA 218 9.33e+00 c.23.10.6 100810 1n7oA 721 9.47e+00 a.102.3.2,b.24.1.1,b.30.5.2 80259,80260,80261 1m1nA 491 9.93e+00 c.92.2.3 78417 1b57A 358 9.98e+00 1dosA c.1.10.2 29177 1vjtA 483 1.00e+01 c.2.1.5,d.162.1.2 100833,100834 1i60A 278 1.02e+01 c.1.15.4 71118 1mdwA 328 1.03e+01 d.3.1.3 84934 1xr4A 509 1.06e+01 2bwfA 77 1.10e+01 4pgaA 337 1.11e+01 4pgaA c.88.1.1 35565 1yzfA 195 1.12e+01 1b74A 254 1.12e+01 1b74A c.78.2.1,c.78.2.1 35264,35265 1b73A 254 1.14e+01 1b74A c.78.2.1,c.78.2.1 35266,35267 1zu4A 320 1.26e+01 1i8tA 367 1.26e+01 c.4.1.3,d.16.1.7 66094,66095 1jf8A 131 1.27e+01 c.44.1.1 66621 1hizA 379 1.28e+01 c.1.8.3 65841 1kkoA 413 1.31e+01 c.1.11.2,d.54.1.1 68675,68676 1t0yA 122 1.33e+01 d.15.1.1 99066 1rpl 251 1.34e+01 1bpyA a.60.12.1,d.218.1.2 75933,75934 1pkhA 204 1.35e+01 b.85.4.1 94832 1bpb 248 1.37e+01 1bpyA a.60.12.1,d.218.1.2 75811,75812 1pz1A 333 1.37e+01 c.1.7.1 95390 1ib2A 349 1.38e+01 1ib2A a.118.1.8 62141 1yfm 488 1.40e+01 1furA a.127.1.1 19413 1fp4A 492 1.41e+01 c.92.2.3 76187 5p21 166 1.41e+01 1ctqA c.37.1.8 31966 1mdoA 393 1.48e+01 c.67.1.4 79013 1f2dA 341 1.48e+01 1f2dA c.79.1.1 35298 1oj6A 151 1.50e+01 a.1.1.2 93088 1vaoA 560 1.52e+01 1qltA d.58.32.1,d.145.1.1 39461,41724 1ezwA 349 1.54e+01 1ezwA c.1.16.3 29558 1ak2 233 1.57e+01 1zin c.37.1.1,g.41.2.1 31894,45195 1w1kA 560 1.61e+01 d.58.32.1,d.145.1.1 109059,109060 1gtzA 156 1.61e+01 c.23.13.1 70539 1nfp 228 1.63e+01 1nfp c.1.16.2 29555 1d0iA 156 1.66e+01 2dhqA c.23.13.1 31383 1mioB 458 1.81e+01 1qguB c.92.2.3 35602 1lucA 355 1.89e+01 1lucA c.1.16.1 29547 1byuA 216 1.90e+01 1byuA c.37.1.8 32032 1sflA 238 1.97e+01 1dosA 358 1.97e+01 1dosA c.1.10.2 29175 1im5A 180 2.00e+01 c.33.1.3 66211 1mw9X 592 2.00e+01 e.10.1.1 91480 1qltA 560 2.02e+01 1qltA d.58.32.1,d.145.1.1 39457,41720 1o9rA 162 2.04e+01 a.25.1.1 86706 1uruA 244 2.08e+01 h.4.14.1 99835 2dorA 311 2.08e+01 2dorA c.1.4.1 28593 1pmd 675 2.09e+01 1pmd d.11.1.1,d.11.1.1,d.175.1.1,e.3.1.1 37491,37492,42562,42771 1ecl 597 2.12e+01 1ecl e.10.1.1 43238 1dorA 311 2.14e+01 2dorA c.1.4.1 28595 1fiy 883 2.19e+01 1fiy c.1.12.3 29307 1j0dA 341 2.19e+01 c.79.1.1 83902 2dhqA 146 2.19e+01 2dhqA c.23.13.1 31382 1mzhA 225 2.20e+01 c.1.10.1 79698 1xqiA 195 2.23e+01 1qd1A 325 2.26e+01 1qd1A d.58.34.1,d.58.34.1 39493,39494 1o20A 427 2.29e+01 c.82.1.1 86556 3aig 202 2.32e+01 1atlA d.92.1.9 40321 1q1gA 276 2.33e+01 c.56.2.1 95574 2cw6A 298 2.36e+01 1s2xA 206 2.44e+01 a.47.3.1 105229 1qb4A 883 2.48e+01 c.1.12.3 74640 1opr 213 2.50e+01 1opr c.61.1.1 34091 1oghA 204 2.55e+01 b.85.4.1 86994 1wc9A 169 2.57e+01 1u02A 239 2.58e+01 c.108.1.15 107538 1kfd 605 2.59e+01 1xwl c.55.3.5,e.8.1.1 33694,42987 1ispA 181 2.59e+01 c.69.1.18 76778 1sfjA 238 2.62e+01 1e8gA 560 2.69e+01 1qltA d.58.32.1,d.145.1.1 39455,41718 1s95A 333 2.69e+01 d.159.1.3 105375 1vgjA 184 2.71e+01 1ur3M 319 2.71e+01 c.1.7.1 99806 1nom 248 2.74e+01 1bpyA a.60.12.1,d.218.1.2 75929,75930 1i6wA 181 2.80e+01 1i6wA c.69.1.18 61859 1nt2B 258 2.85e+01 a.183.1.1 86150 2bijA 305 2.87e+01 1vpgA 192 2.92e+01 1gdhA 320 2.93e+01 1gdhA c.2.1.4,c.23.12.1 30095,31355 1jx2B 315 2.98e+01 c.37.1.8 67404 2aq4A 434 3.02e+01 1tv8A 340 3.04e+01 c.1.28.3 107352 1ex1A 605 3.09e+01 1ex1A c.1.8.7,c.23.11.1 29013,31347 1j6uA 469 3.15e+01 c.5.1.1,c.59.1.1,c.72.2.1 77094,77095,77096 2ftwA 521 3.15e+01 1dekA 241 3.19e+01 1dekA c.37.1.1 31842 1fljA 260 3.19e+01 2cba b.74.1.1 27954 1h05A 146 3.19e+01 c.23.13.1 76433 1dbuA 158 3.20e+01 1dbuA d.116.1.1 40930 1jndA 420 3.23e+01 c.1.8.5,d.26.3.1 71757,71758 2bvlA 543 3.24e+01 1vmjA 151 3.27e+01 1lzlA 323 3.29e+01 c.69.1.2 78306 1j0aA 325 3.32e+01 c.79.1.1 83871 1yxyA 234 3.32e+01 1sazA 381 3.34e+01 2b7kA 200 3.41e+01 1f74A 293 3.52e+01 1nal3 c.1.10.1 29079 1ohvA 472 3.52e+01 c.67.1.4 93031 1tv9A 335 3.53e+01 1fj7A 101 3.63e+01 1fj7A d.58.7.1 39209 1g19A 350 3.66e+01 2reb c.37.1.11,d.48.1.1 32284,38770 1d9eA 284 3.78e+01 1d9eA c.1.10.4 29195 1h5qA 265 3.82e+01 1cydA c.2.1.2 60643 1jmvA 141 3.84e+01 c.26.2.4 66897 1lxnA 99 3.85e+01 d.58.48.1 84737 1b0aA 288 3.90e+01 1a4iA c.2.1.7,c.58.1.2 30286,33934 1tr1A 447 3.96e+01 1e70M c.1.8.4 28957 1gtxA 472 4.03e+01 1gtxA 2bsxA 253 4.14e+01 1vqoO 116 4.19e+01 1jubA 311 4.19e+01 c.1.4.1 90908 1delA 241 4.22e+01 1dekA c.37.1.1 31844 1fjgC 239 4.26e+01 1fjfC d.52.3.1,d.53.1.1 38831,38839 1q1fA 151 4.26e+01 a.1.1.2 104476 1oxsC 353 4.27e+01 b.40.6.3,c.37.1.12 87519,87520 1e4iA 447 4.28e+01 1e70M c.1.8.4 59225 1jqnA 883 4.31e+01 c.1.12.3 77159 1fdd 106 4.37e+01 1a6l d.58.1.2 38960 1qspA 165 4.41e+01 1qspA a.24.10.2 16639 1ajsA 412 4.42e+01 1ajsA c.67.1.1 34276 1ra6A 461 4.46e+01 e.8.1.4 104879 1lg2A 365 4.47e+01 c.1.8.5,d.26.3.1 77950,77951 1hkkA 364 4.48e+01 c.1.8.5,d.26.3.1 90634,90635 1dugA 234 4.49e+01 1b8xA a.45.1.1,c.47.1.5 17718,33012 1x38A 602 4.52e+01 1g6aA 271 4.55e+01 1btl e.3.1.1 42704 1uz1A 468 4.56e+01 1jfvA 131 4.60e+01 c.44.1.1 66654 1j5eC 239 4.70e+01 d.52.3.1,d.53.1.1 71544,71545 1rzmA 338 4.72e+01 c.1.10.4 105137 2gaiA 633 4.73e+01 1b8xA 280 4.74e+01 1b8xA a.45.1.1,c.47.1.5 17739,33033 1f6fA 199 4.76e+01 1f6fA a.26.1.1 16839 1cliA 345 4.81e+01 1cliA d.79.4.1,d.139.1.1 39816,41459 2g45A 129 4.81e+01 1kagA 173 4.83e+01 c.37.1.2 72249 2b6cA 220 4.84e+01 1fjeB 175 4.87e+01 1fj7A d.58.7.1,d.58.7.1 39210,39211 1iexA 605 4.89e+01 c.1.8.7,c.23.11.1 66127,66128 1gudA 288 4.90e+01 c.93.1.1 83326 1bxkA 355 4.92e+01 1bxkA c.2.1.2 29803 2aclB 244 4.98e+01 1y2qA 143 4.99e+01 1a7j 290 5.01e+01 1a7j c.37.1.6 31952 1kgnA 329 5.01e+01 a.25.1.2 68584 1xknA 355 5.01e+01 1zcoA 262 5.08e+01 1zuwA 272 5.10e+01 1c02A 166 5.12e+01 1qspA a.24.10.2 16633 1a6l 106 5.14e+01 1a6l d.58.1.2 38966 1jj2N 115 5.15e+01 1ffkL c.12.1.1 63099 1gesA 450 5.29e+01 3grs c.3.1.5,c.3.1.5,d.87.1.1 30473,30474,40168 1w6uA 302 5.30e+01 2b1xA 470 5.36e+01 1ufoA 238 5.39e+01 c.69.1.27 99344 1aoa 275 5.41e+01 1aoa a.40.1.1,a.40.1.1 17396,17397 1knwA 425 5.56e+01 b.49.2.3,c.1.6.1 90969,90970 1pa7A 130 5.56e+01 a.40.1.1 94410 2c4wA 176 5.56e+01 1bt0A 76 5.62e+01 1ubi d.15.1.1 37607 1pnsC 206 5.67e+01 i.1.1.1 88170 1allA 160 5.74e+01 1qgwC a.1.1.3 15647 2c07A 285 5.76e+01 1oxxK 353 5.84e+01 b.40.6.3,c.37.1.12 93715,93716 8abp 306 5.85e+01 8abp c.93.1.1 35647 1hjsA 332 5.90e+01 c.1.8.3 83492 1dofA 403 5.91e+01 1c3cA a.127.1.1 19429 1jmeA 455 5.95e+01 a.104.1.1 66885 1xpjA 126 5.96e+01 1vr6A 350 5.97e+01 1r5rA 119 5.98e+01 a.39.2.1 97104 1glqA 209 6.02e+01 1pgtA a.45.1.1,c.47.1.5 17588,32882 1cjtA 217 6.04e+01 1azsA d.58.29.1 39419 1hg3A 225 6.07e+01 1hg3A c.1.1.1 61025 1aqwA 209 6.08e+01 1pgtA a.45.1.1,c.47.1.5 17517,32811 1e6pA 499 6.09e+01 1e15A b.72.2.1,c.1.8.5,d.26.3.1 59314,59315,59316 1rcd 173 6.09e+01 2fha a.25.1.1 16687 1e15A 499 6.10e+01 1e15A b.72.2.1,c.1.8.5,d.26.3.1 27810,29006,38440 1fobA 334 6.11e+01 c.1.8.3 83255 1aoqA 567 6.23e+01 1qksA a.3.1.2,b.70.2.1 15934,27692 1necA 216 6.24e+01 1vfrA d.90.1.1 40249 1r0dA 206 6.32e+01 a.216.1.1 104715 1s14A 194 6.33e+01 d.122.1.2 98329 1fzqA 181 6.34e+01 1hurA c.37.1.8 32060 1jwyB 315 6.36e+01 c.37.1.8 67401 1sz7A 200 6.37e+01 1w3jA 468 6.42e+01 c.1.8.4 109156 1vkmA 297 6.44e+01 c.138.1.1 108670 5abp 306 6.49e+01 8abp c.93.1.1 35651 2phh 394 6.49e+01 1pbe c.3.1.2,d.16.1.2 30353,37884 1t0hB 224 6.50e+01 c.37.1.1 106208 1shkA 173 6.51e+01 1shkA c.37.1.2 31932 1wwkA 307 6.52e+01 1viwB 198 6.52e+01 1led b.29.1.1 24170 1pjjA 271 6.61e+01 a.156.1.2,b.113.1.1,g.39.1.8 104164,104165,104166 1jr3A 373 6.61e+01 a.80.1.1,c.37.1.20 63245,63246 2cbuA 468 6.61e+01 1edt 271 6.66e+01 2ebn c.1.8.5 28993 1g8pA 350 6.66e+01 1g8pA c.37.1.20 60376 1kafA 108 6.69e+01 d.199.1.1 68372 7fd1A 106 6.69e+01 1a6l d.58.1.2 38953 1vdeA 454 6.74e+01 1vdeA b.86.1.2,d.95.2.2,d.95.2.2 28378,40581,40582 1t3lA 337 6.77e+01 b.34.2.1,c.37.1.1 106358,106359 1sg6A 393 6.78e+01 e.22.1.1 105522 1qksA 567 6.93e+01 1qksA a.3.1.2,b.70.2.1 15951,27710 1s72O 116 6.96e+01 c.12.1.1 105334 1bap 306 6.96e+01 8abp c.93.1.1 35654 1dvjA 246 7.07e+01 1dvjA c.1.2.3 28546 1bpyA 335 7.09e+01 1bpyA a.60.6.1,a.60.12.1,d.218.1.2 17980,75819,75820 1jbbA 153 7.12e+01 1u9aA d.20.1.1 62842 1wb0A 445 7.15e+01 1t3gA 159 7.22e+01 1e6cA 173 7.22e+01 1shkA c.37.1.2 59296 1abe 306 7.24e+01 8abp c.93.1.1 35648 1lbkA 208 7.31e+01 a.45.1.1,c.47.1.5 73809,73810 1e5eA 404 7.37e+01 1ibjA c.67.1.3 59265 1kn1A 160 7.41e+01 a.1.1.3 77455 1vykA 149 7.42e+01 2shkA 173 7.49e+01 1shkA c.37.1.2 31934 1pqxA 91 7.49e+01 d.267.1.1 104296 2g76A 335 7.56e+01 1o94A 729 7.56e+01 c.1.4.1,c.3.1.1,c.4.1.1 81200,81201,81202 1dn1B 267 7.58e+01 1dn1B a.47.2.1 17771 1i5nA 146 7.62e+01 1i5nA a.24.10.3 61805 1m2oB 190 7.80e+01 c.37.1.8 78485 1j7lA 264 7.85e+01 d.144.1.6 62697 1mugA 168 7.85e+01 1mugA c.18.1.2 31030 1gehA 444 7.86e+01 c.1.14.1,d.58.9.1 65181,65182 1ydgA 211 7.90e+01 1jdlA 121 7.91e+01 a.3.1.1 66557 1vkyA 347 7.94e+01 e.53.1.1 108696 1acc 735 7.96e+01 1acc f.11.1.1 43828 1k4nA 192 7.98e+01 d.32.1.5 72059 1jl3A 139 7.99e+01 c.44.1.1 66826 1pgtA 210 7.99e+01 1pgtA a.45.1.1,c.47.1.5 17515,32809 2b99A 156 8.05e+01 1dtdA 303 8.16e+01 1aye c.56.5.1 33823 1ybzA 91 8.17e+01 1zy9A 564 8.27e+01 2av4A 162 8.33e+01 1al3 324 8.48e+01 1al3 c.94.1.1 35835 1azsA 220 8.57e+01 1azsA d.58.29.1 39416 2bhuA 602 8.61e+01 1u55A 188 8.64e+01 d.278.1.1 107677 1p80A 753 8.69e+01 c.23.16.3,e.5.1.1 94337,94338 1kzyC 259 8.71e+01 c.15.1.4,c.15.1.4 73383,73384 1nnhA 294 8.74e+01 d.104.1.1 92005 1jmxB 349 8.75e+01 b.69.2.2 66906 1r6uA 437 8.75e+01 c.26.1.1 97163 1p7gA 222 8.76e+01 a.2.11.1,d.44.1.1 94223,94224 1bgj 394 8.79e+01 1pbe c.3.1.2,d.16.1.2 30352,37883 1fmjA 351 8.83e+01 c.37.1.5 59879 1x1zA 252 8.84e+01 1lyxA 248 8.87e+01 c.1.1.1 78304 1kwhA 492 8.90e+01 c.94.1.1 68876 1w77A 228 8.91e+01 2af8 86 8.92e+01 2af8 a.28.1.1 16933 1b8bA 605 8.95e+01 1b8bA